amplicR: amplicR

amplicRR Documentation

amplicR

Description

An R package to process amplicon data.

Details

This package has a number of functions to filter, dereplicate and error and chimera check NGS reads stored in fastq files. This funcitonality is currently limted to single-read analysis. The retained reads after the data processing described above (or your own reads if you have done this already in another way) can then be compared against reference sequences and the number of mismatch is reported. This may be useful when, for example, screening samples for particular taxa (e.g. a pathogen).

amplicR is mainly a wrapper of several functions provided by other R packages in order to automate some common analyses, so if you use it, please make sure to also cite the relevant packages (these are generally indicated in the documentation of amplicR's functions). To find out the correct citation for a package, you can use the function: citation("package_name") where you have to replace package_name with the actual name of the package you are interested into.

Documentations

Use help(package = "amplicR") for a list of amplicR functions and their specific documentations.

A more detailed description of the package and functions can be opened with:

vignette(package="amplicR", topic="amplicR-package") - This is pending... hang in there

Citation

If you use amplicR, please cite:

This is also pending

Get in touch

Please, use https://github.com/carlopacioni/amplicR/issues to report any issues with amplicR. If unsure, or for feedback, contact me at: carlo.pacioni 'at' gmail.com.


carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.